Migrating to letsencrypt for sites on Ubuntu 14.04

Hi,
My existing ISPconfig3 has been working great. I am now running on 3.1.1p1 on Ubuntu 14.04.5 on a Linode. Server install was done a year or two ago using the perfect server procedure.
Up till now, the various sites I run have SSL certs obtained via StartSSL. Last year, I paid for a Class 2 IV so I can generate my certs and all was going well. However, since the buyout by WoSign and the now distrust, any new certs I create will no longer be trusted by latest versions of browsers, so I'm looking at migrating to another CA. Due to the number of domains I have, this could be quite costly so I'm investigating using LetsEncrypt as an alternative.

I've had a quick play, but before I really try things in anger and fear breaking my sites... What I've done so far:
from /opt/:

Thaks sjau,
In the end, as the server is on Linode and had less than half the storage assigned, I cloned the disk to have a fallback backup and then tried an upgrade which seems to have pretty much worked. I'm now on Ubuntu 16 and was able to install the letsencrypt package and it seems to be functioning OK - I've had a new cert delivered and installed through ISPconfig